Setting up a multi-factor experiement
Entering edit mode
Last seen 13 hours ago
United States


I am rerunning some bulk samples thru my pipeline, but am including more samples from various organs of individuals from either sex and also considering symbiotic state. My All.coldata looks like this:

> All.coldata
                 Seq.Batch Symbiotic.State Tissue.Type Sex
FS11_WBL                 2             SYM         WBL   F
FS13_WBL                 1             SYM         WBL   F
FS15_WBL                 1             SYM         WBL   F
FT21_WBL                 2             SYM         WBL   F
FU3_WBL                  2             SYM         WBL   F
MS4_WBL                  1             SYM         WBL   M
MT13_WBL                 2             SYM         WBL   M
MT14_WBL                 2             SYM         WBL   M
MT20_WBL                 2             SYM         WBL   M
MT8_WBL                  2             SYM         WBL   M
FS13_OLL                 1             SYM         OLL   F
FS15_OLL                 1             SYM         OLL   F
FU3_OLL                  2             SYM         OLL   F
MS3_OLL                  1             SYM         OLL   M
MS4_OLL                  1             SYM         OLL   M
MT8_OLL                  2             SYM         OLL   M
FS15_CB                  1             SYM          CB   F
FT12_CB                  2             SYM          CB   F
FU3_CB                   2             SYM          CB   F
MT13_CB                  2             SYM          CB   M
MT6_CB                   2             SYM          CB   M
MT8_CB                   2             SYM          CB   M
FSJM26_WB                2             APO          WB   F
FSJM61_WB                2             APO          WB   F
FSJM63_WB                2             APO          WB   F
FS11_MNTL_190922         2             SYM        MNTL   F
FU3_MNTL_190931          2             SYM        MNTL   F
MS3_MNTL                 1             SYM        MNTL   M
MS4_MNTL                 2             SYM        MNTL   M
MT13_MNTL_190910         2             SYM        MNTL   M

And I'm wondering how best to set up my dds. I've run an analysis before where I consider just Tissue.Type, but I want to think about how sex and symbioses plays a part in the DE as well. Should I run DESeq just comparing tissue.type then add in the design(ddsMF) <- formula(~ type + condition) for multi-factor design and include the other columns of my All.coldata ?

Please let me know what you think, thanks!

And my sessioninfo() is:

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7.8

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.2.2    fastmap_1.1.1     Matrix_1.5-4      limma_3.54.2      cli_3.6.1        
 [6] htmltools_0.5.6   tools_4.2.2       rstudioapi_0.15.0 yaml_2.3.7        rmarkdown_2.24   
[11] grid_4.2.2        knitr_1.43        xfun_0.40         digest_0.6.33     rlang_1.1.1      
[16] evaluate_0.21     lattice_0.21-8
DESeq2 • 187 views
Entering edit mode
Last seen 9 hours ago
United States

For questions about statistical analysis plan, I recommend to work with a local statistician or someone familiar with linear models in R.

Entering edit mode

thanks, will do! we work with a non-model organism, but perhaps the folks who do our genomics/sequencing have some input.


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